Using qiagen kit for ChIP DNA purification - (May/27/2005 )

I use Qiagen PCR product purification kit instead of phenol-chloroform after reverse crosslinking crhomatin. Is it a good idea? Does anyone has any experience with using this kit for ChIP?

-CHIPMAN3-

I thought of using it too, but have not because of uncertainty. Please let us know if it works.

-pcrman-

I did use QiaEx II gel extraction kit for ChIP.

First of all, I have to mention that I still haven't solved the unspecific bands in No AB ctrl issue. In order to follow another person's protocol, who used the Ab that I am using, I religously followed his way of purification as well, which is P/C/I. The result is: the result of the purification methods didn't seem to differ.

I start with 10-20 million cells. And decross link only 1/3 of the input. One thing about using the QiaEx to clean up is using 5 ul of the beads for IP samples and 10 ul for Input ctrl.

Hope it helps those of you who want to save time

-koira-

Hi koira,

Thanks for sharing your result.

How many PCR cycles do you usually run for your Ab and no-Ab samples? If too many cycles are used, anything may turn positive. I would say keep the number of cycles below 30.

-pcrman-

25.I think I may need to optimize the cycle numbers. Thanks for your suggestion